Advances in protein separation technologies and innovations in MS (mass spectrometry) have greatly increased whole genome approaches in biology. However the explosion of information in the fields of genomics and proteomics has not been matched by a corresponding advancement of knowledge in the field of organellar proteomics, lipids and glycans, which is largely due to the structural complexity and the lack of powerful tools for their analysis. Hence, it has become more apparent that whole cells and tissues are not currently amenable to satisfactory whole “Omics” analysis. This is due to complexity and extreme dynamic range of protein expression in a whole cell (for example less abundant proteins are masked by those expressed at higher levels).
However, whole “Omics” analysis of subcellular compartments is hampered by difficulties inherent in purifying organelles as disclosed in Dreger (2003) Mass Spectrom. Rev. 22(1), 27-56. Particularly the analysis or proteins, lipids and carbohydrates in the plasma membrane and endosomal/lysosomal compartment system (EE/Lys) poses major hurdles as it is most dynamic in nature with strongly overlapping buoyant densities making it impossible to physically separate closely related populations. In addition, effective isolation and protein purification from subcellular compartments is the most crucial step for a whole genome analysis where only minute quantities are available. However, even the best optimized conventional purification methods such as density gradient centrifugation and colloidal silica based plasma membrane fractionation often lead to only partially purified compartments [Arjunan (2009) Cell Biochem. Biophys. 53(3), 135-143.].
Magnetic particles with targeting groups, such as antibodies have been used to isolate particular proteins or cells. Lipid coated magnetic particles have been used to deliver substances intracellularly. The use of such magnetic particles for the isolation of distinct cell membranes, such as e.g. plasma membrane and endosomes/lysosomes is unexplored. The present inventors disclosed the advantageous properties of a magnetic particle that would remain associated with a plasma membrane but are silent on the composition of beads that would have such properties [Nanotech Montreux meeting 17-19 Oct. 2008].
Other attempts to isolate plasma membrane derived endosomes are described in e.g. Rivière et al. (2007) Eu. Phys J. E. soft matter 22, 1-10 wherein magnetic particles are used which are not homogenous in size, resulting in an inefficient isolation process with low yield and purity and contamination with plasma membranes.